Biology Reference
In-Depth Information
designed to address both issues: first to deliver the most accurate
possible MSAs, and second to estimate the accuracy of MSAs
delivered by T-Coffee or alternative aligners.
2 Materials
2.1 T-Coffee
Web Server
T-Coffee is available through a Web server
http://tcoffee.crg.cat/
apps/tcoffee/index.html
[
7
] which contains the same modes as
T-Coffee package; however it has limited capabilities regarding
the size of your dataset (max 150 sequences) and the length of
your sequences (2,500 characters). It is well suited for routine
alignment but for more sophisticated or complex alignment, users
should use the T-Coffee package. This chapter focuses only on a
detailed explanation on how T-Coffee package can be used in its
command line mode [
8
].
T-Coffee is distributed as precompiled binaries for Linux and Mac
OS X platforms with a guided install procedure. This is the smooth-
est and quickest way to install T-Coffee on a local machine, since it
comes with all required components and does not need any special
user privilege. The Windows operating system is no longer sup-
ported; however users working on that environment can use a
Linux station working in a virtual environment such as VMware.
Most Linux distributions should work, especially Fedora, Debian,
and Ubuntu being the most thoroughly tested (
see Note 1
). It is
also possible to compile the source code under the Cygwin envi-
ronment within a Windows operating system.
2.2 Computational
Requirement
2.3
Installation
On Linux
- Download the installer package from the following URL:
- Grant execution permission to the downloaded file:
chmod +x T-COFFEE-installer-
version-xxx
.bin
<
>
- Launch the installation wizard with
./T-COFFEE-installer-
.bin
- Follow the wizard instructions and complete the installation.
version-xxx
<
>
On Mac OS X
- Download the installer package from the following URL:
- Double click on the DMG file to open it.
- Double click on the installer icon (within the mounted image).
- Follow the wizard instructions and complete the installation.
